陆雅海. 土壤微生物学研究现状与展望[J]. 中国科学院院刊, 2015, 30(Z1): 106-114
Lu Yahai. Recent Development of Soil Microbiology and Future Perspectives[J]. Bulletin of Chinese Academy of Sciences, 2015, 30(Z1): 106-114
北京大学城市与环境学院 北京 100871
关键词： 土壤微生物学 微生物多样性 生物地球化学循环 国际土壤年
Recent Development of Soil Microbiology and Future Perspectives
College of Urban and Environmental Sciences, Peking University, Beijing 100871, China
Corresponding author: Lu Yahai,is a Changjiang Scholar Professor in Peking University. He obtained the National Science Fundfor Distinguished Young Scholars in2006. His researches have been focused on soil microbiology and biogeochemistry. The major advances he has achieved in the past decade include: the improvement of microbial stableisotope probing technology and its applications to rhizosphere and soil microbiology; the delineation of microbial community successions during the degradation of plant residues in anoxic rice field soil; the identificationof key organisms involved in the syntrophic oxidation of major fatty acids intermediates; the isolation of a novel methanogen species and the characterization of its key function in methanogenesis in rice field soil; the elucidation of the effects of the field managements on methanotrophs and methane oxidation. He has served as theeditorial board member for Applied and Environmental Microbiology, FEMS Microbiology Ecology, MicrobialEcology, and Soil Science and Plant Nutrition. E-mail: email@example.com
Abstract:Soil is the living skin of the Earth, where inhabit numerous kinds of life, including bacteria, archaea, fungi, protozoa, invertebrates, arthropods, plants, and higher animals. They constitute a food web forming unique ecological networks sustaining the terrestrial ecosystem functioning. The diverse metabolic mechanisms of microbes serve as the core engines that drive the earth's element biogeochemical cycles. Microbial activities play the key roles in soil formation, the development of soil fertility, the remediation of soil contaminations, and the protection of soils from erosion and degradation. They also regulate the fluxes of greenhouse gases between the atmosphere and the earth. It is the soil microbiota that make soils highly active in energy and material exchanges with the atmosphere, the biosphere, the hydrosphere, and the lithosphere. The investigations into microbial diversity in soils, however, have largely lagged behind historically due to methodological limitations. Soil microbiology as a branch and a cross discipline between soil science and biology has been developed in the late nineteenth century. The development has been mainly based on the cultivation-dependent methods, including enrichment cultivation, purification and isolation, and physiological and biochemical examinations. These methods have been recognized as hallmarks in soil microbiology. Unfortunately, they are incapable to fully explore the diversity of soil microorganisms. Inevitably, the microbial diversity and function in soils have been under appreciated for over a century. It is until the early 90s of the last century that the cultivation- independent techniques has been developed and applied to soil microbiology. Various techniques, based on microbial DNA analyses, like cloning and sequencing, denaturing gradient gel electrophoresis and terminal restriction fragment length polymorphism analysis were invented that provided a new dimension of soil microbiota investigations. It is well understood now that the cultivatable microbes account for only less than 1% of the total microbes in soils. To explore the diversity and function of the uncultivated organisms, the new generation of molecular technologies including high throughput sequencing and single cell technology is being developed. Novel cultivation techniques targeting the difficult-to-cultivate organisms are also under development. Overall, the beginning of the 21th century marks an unprecedented revolution of soil microbiology. The 2015 International Year of Soils is an occasion to celebrate the development of soil science and raise the awareness of Earth's soil and its function to humanity. It is a great opportunity to prepare a review on the progresses of soil microbiology, which is perhaps by far the fastest developing subdiscipline of soil sciences in the last few decades. Due to the space and knowledge limits, however, it is impossible to give a comprehensive review on this topic. Instead, in this review I focused only to a few selected topics. Firstly, I discussed the exponential expanding of the understanding of soil microbial diversity. Microbial diversity is the core theme in soil microbiology. Understanding the vast diversity is the basis for predicting and managing the functioning of soil microbiota. The expanding of this field is largely facilitated by the rapid evolution of molecular ecological technologies. Secondly, I outlined the major advances in deciphering the microbial mechanisms for C and N biogeochemical cycles. Microbial C and N transformations are closely related to soil fertility and greenhouse gas production. These processes also influence the environmental quality. Many advances have been achieved in the past decades in identifying the key microbes and mechanisms of both C and N cycling in soil. The pathways of microbial C and N transformations are basically different between upland soils and water-lodged soils and hence are discussed separately. Thirdly, an overview of the development of soil microbiology in China is given. Since the last decade, the National Natural Science Foundation of China has focused a special attention to soil microbiology. This has greatly promoted the development of this field in China. Lastly, I put forward a few suggestions and challenges for the further development of soil microbiology. These include the scaling of microbial processes from the molecular level to the ecosystem level and beyond, elucidating the mechanisms and theories of microbial adaptations to environmental changes, identifying the novel organisms and pathways of microbial C and N transformations, and the further development and innovation of methodology for soil microbiology.